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ababaian / LIONS

LIONS is a bioinformatic analysis pipeline which brings together a few pieces of software and some home-brewed scripts to annotate a paired-end RNAseq library to detect TE-intiated transcripts
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chimGroup.R Error in `$<-.data.frame`(`*tmp*`, "RMDB", #2

Closed qoldt closed 5 years ago

qoldt commented 6 years ago

Hi Artem, When running Westlions.sh I'm getting a data.frame error in R. It seems an extra row is being generated:

Rscript chimGroup.R ../../input.list ../../rmStats.Rdata 1 1
[1] " Running standard analysis"
Error in `$<-.data.frame`(`*tmp*`, "RMDB", value = c(249320L, 302633L,  : 
replacement has 9538 rows, data has 9537
Calls: $<- -> $<-.data.frame
In addition: Warning message:
In `[<-.data.frame`(`*tmp*`, "Group", value = list(numeric(0), numeric(0),  :
provided 9537 variables to replace 1 variables
Execution halted
ababaian commented 6 years ago

Would you be able to email me the input data? I'd like to run this line-by-line to figure out where the error is arising.

ababaian commented 6 years ago

I guess I should clarify @qoldt, the chimGroup.R input data (they are much smaller files) input.list WT.lion ( for each replicate) DKO.lion (for each replicate) parameter.ctrl rmStats.Rdata

It might be that the input.list data was all a single group (column 3). West Lions is for comparing sets of .lion files (set level differences).

b12loroc commented 6 years ago

Hi Artem, when running east lion with fastq file, exist an error with tophat, if i running lions with bam file it happens the same that @qoldt to me

ababaian commented 6 years ago

I can't seem to replicate the error. As I'm running the script it goes through and produces the output successfully.

One thing I had to change though was making the input.list file tab-separated instead of space separated for it to be read. Can you try changing that and re-running?

b12loroc commented 6 years ago

i have already run lions with input.list file tab-separated and lions didn´t detect paired fastq file, althought i separated input with comma. Running tophat2 ... cmd: /mnt/home/users/pab_001_uma/b12loroc/Protocolo/Experimento/LIONS_171220/bin/tophat2 -p 1 -r 50 --report-secondary-alignments -o /mnt/home/users/pab_001_uma/b12loroc/Protocolo/Experimento/LIONS_171220/pr ojects/sandboxadenocarcinoma/paciente1tumor hg38_illumina /mnt/home/users/pab_001_uma/b12loroc/Protocolo/Experimento/LIONS_171220/projects/sandboxadenocarcinoma/paciente1tumor/temp.1.fq.gz /mnt/home/users/pab_00 1_uma/b12loroc/Protocolo/Experimento/LIONS_171220/projects/sandboxadenocarcinoma/paciente1tumor/temp.2.fq.gz File "/mnt/backup/soft/tophat/programs/x86_64/2.0.13/tophat", line 1001 except getopt.error, msg: ^ SyntaxError: invalid syntax du: cannot access `accepted_hits.bam': No such file or directory /mnt/home/users/pab_001_uma/b12loroc/Protocolo/Experimento/LIONS_171220/scripts/eastLion.sh: line 195: [: -ge: unary operator expected Alignment probably didnt work Cheers and thanks!

2018-03-01 17:10 GMT+01:00 Artem Babaian notifications@github.com:

I can't seem to replicate the error. As I'm running the script it goes through and produces the output successfully.

One thing I had to change though was making the input.list file tab-separated instead of space separated for it to be read. Can you try changing that and re-running?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/ababaian/LIONS/issues/2#issuecomment-369642035, or mute the thread https://github.com/notifications/unsubscribe-auth/Af3ejMDexeOquHdswvCOKYIafXdHLCohks5taB18gaJpZM4SMO76 .

qoldt commented 6 years ago

@b12loroc it looks like you have other issues. This thread is specifically about a problem in the westlion.sh script.

I deleted all the files, made sure input.list was tab delimited (using vi), and ran everything from the beginning again. Still the problem remains.

I looked at the relevant part of the Rscript and it looks good to me. Today I will try troubleshooting it locally. I'll let you know if I figure it out.

ababaian commented 6 years ago

@qoldt did you find a solution to this?

qoldt commented 6 years ago

I did find this thread that dealt with the issue, but I couldn't resolve it in this context. For now I have written an R script specific to my experiment to filter the .lions file down to those that occur consistently in treatment conditions. I may write to you later to inquire about custom settings (vs using screenTE or driverTE) as presently it is not picking up couple chimeras that I have found using a running window on the bam files in seqmonk.

biscuit13161 commented 5 years ago

@ababaian it seems likely that this is related to the input.list issue I fixed here: https://github.com/ababaian/LIONS/issues/14